BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716466.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 3,495,792 number of mapped reads = 3,177,582 (90.9%) number of supplementary alignments = 17,405 (0.5%) number of secondary alignments = 0 number of mapped bases = 187,994,843 bp number of sequenced bases = 187,939,500 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 171,680 duplication rate = 4.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.476 >>>>>>> ACTG content number of A's = 49,543,441 bp (26.36%) number of C's = 38,201,896 bp (20.33%) number of T's = 57,158,963 bp (30.41%) number of G's = 43,029,952 bp (22.9%) number of N's = 5,248 bp (0%) GC percentage = 43.22% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 932,637 number of insertions = 14,291 mapped reads with insertion percentage = 0.45% number of deletions = 34,915 mapped reads with deletion percentage = 1.09% homopolymer indels = 40.04% >>>>>>> Coverage mean coverageData = 0.0607X std coverageData = 0.4765X There is a 4.98% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 15131212 0.06070681765723665 0.943632882550483 chr2 243199373 15861777 0.06522129068153477 0.5666114545335075 chr3 198022430 12559860 0.06342645123585243 0.3006686365536925 chr4 191154276 12093035 0.06326321991353204 0.3321233470373962 chr5 180915260 11349170 0.06273196633606253 0.2993551123967352 chr6 171115067 10931581 0.06388438605467746 0.38118986024842594 chr7 159138663 10322863 0.06486709643903443 0.5946064577634026 chr8 146364022 9459838 0.0646322632484095 0.4401234935231726 chr9 141213431 7812766 0.05532594134052306 0.3926151346658697 chr10 135534747 9016555 0.06652578176133682 0.46102582907307416 chr11 135006516 8484090 0.06284207793348286 0.40698389848395006 chr12 133851895 8543922 0.06383116204667853 0.3074430371220621 chr13 115169878 5956896 0.0517226908931865 0.2670555732092111 chr14 107349540 5715917 0.05324584530124675 0.30755870696842175 chr15 102531392 5409464 0.05275910035435782 0.27949634983863475 chr16 90354753 5482566 0.06067822464192891 0.3205109891951902 chr17 81195210 5144229 0.0633563112897916 0.3276726835463794 chr18 78077248 4998097 0.064014769065631 0.7512562502055203 chr19 59128983 3856361 0.06521947113482401 0.6835803172444732 chr20 63025520 3969996 0.06299029345573032 0.30541743504134666 chr21 48129895 2444878 0.05079749290955237 0.3098851723444567 chr22 51304566 2227213 0.04341159420391549 0.24540002427428512 chrMT 16571 27779 1.6763623197151651 1.5906820647648794 chrX 155270560 10633573 0.06848415436899306 0.3525993328687284 chrY 59373566 561205 0.00945210196739741 0.2321625414356765